Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils

Culture-dependent and culture-independent methods were used to investigate the diversity of three polycyclic aromatic hydrocarbon (PAH) catabolic genes in contaminated soils. PAH-degrading bacteria were isolated based on growth at the expense of naphthalene (44 isolates) or phenanthrene (35 isolates). Of these 79 PAH-degraders, 53% (42 isolates) failed to hybridise with three gene probes specific for PAH degradation. The gene for the naphthalene dioxygenase iron–sulfur protein (nahAc) from Pseudomonas putida G7 hybridised to 45% (20/44) of the culturable naphthalene-degrading bacteria of the ‘classical’nah-type, whilst analogues of the bacterial glutathione S-transferase (GST) encoding gene of Sphingomonas paucimobilis EPA505 were associated with culturable phenanthrene-degrading isolates and hybridised to 29% (10/35) of these isolates. Apart from the host strain Burkholderia RP007, we were not able to detect the phnAc gene amongst cultured isolates by hybridisation or PCR, though could directly amplify this gene from contaminated soils.